Salt-dependent DNA-DNA spacings in intact bacteriophage λ reflect relative importance of DNA self-repulsion and bending energies

Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage λ with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5×10(3) base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In the commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1kT/bp, an order of magnitude larger than the bending energies.     

Removal and recovery of mercury from aqueous solution using magnetic silica nanocomposites

Thiol-functionalized magnetic silica nanocomposite was synthesized and tested for its mercury pick-up capability in aqueous solution. Magnetic property was to be utilized upon the collection of the adsorbents and the recovery adsorbed Hg by subsequent separation process. Cobalt ferrite nanoparticle, the core of magnetic silica nanocomposite, was synthesized using a thermal decomposition method and grown to a particle having an average size of 13 nm. The dispersed nanoparticles were then further arranged into spherical groups using a nanoemulsion method to enhance the reactivity toward magnets followed by tetraethyl orthosilicate coating using a modified Stöber method. The pore structure was modified by an additional coating of cetyltrimethylammonium bromide and tetraethyl orthosilicate. Finally, the surface of the magnetic silica nanocomposite was functionalized with thiol group. When tested for mercury adsorption capacity, a sufficiently high Hg adsorption capacity of 19.79 mg per g of adsorbent was obtained at room temperature and a pH of 5.5.     

Synthesis of Multifunctional Mn‐Doped CdTe/ZnS Core/Shell Quantum Dots

The synthesis of a novel water‐soluble Mn‐doped CdTe/ZnS core‐shell quantum dots using a proposed ultrasonic assistant method and 3‐mercaptopropionic acid (MPA) as stabilizer is descried. To obtain a high luminescent intensity, post‐preparative treatments, including the pH value, reaction temperature, reflux time and atmosphere, have been investigated. For an excellent fluorescence of Mn‐doped CdTe/ZnS, the optimal conditions were pH 11, reflux temperature 100°C and reflux time 3 h under N₂ atmosphere. While for phosphorescent Mn‐doped CdTe/ZnS QDs, the synthesis at pH 11, reflux temperature 100°C and reflux time 3 h under air atmosphere gave the best strong phosphorescence. The characterizations of Mn‐doped CdTe/ZnS QDs were also identified using AFM, IR, powder XRD and thermogravimetric analysis. The data indicated that the photochemical stability and the photoluminescence of CdTe QDs are greatly enhanced by the outer inorganic ZnS shell, and the doping Mn²⁺ ions in the as‐prepared quantum dots contribute to strong luminescence. The strong luminescence of Mn‐doped CdTe/ZnS QDs reflected that Mn ions act as recombination centers for the excited electron‐hole pairs, attributing to the transition from the triplet state (⁴T₁) to the ground state (⁶A₁) of the Mn²⁺ ions. All the experiments demonstrated that the surface states played important roles in the optical properties of Mn‐doped CdTe/ZnS core‐shell quantum dots.     

The size of RNA as an ideal branched polymer

Because of the branching arising from partial self-complementarity, long single-stranded (ss) RNA molecules are significantly more compact than linear arrangements (e.g., denatured states) of the same sequence of monomers. To elucidate the dependence of compactness on the nature and extent of branching, we represent ssRNA secondary structures as tree graphs which we treat as ideal branched polymers, and use a theorem of Kramers for evaluating their root-mean-square radius of gyration, ?R(g)=√R(g)(2). We consider two sets of sequences--random and viral--with nucleotide sequence lengths (N) ranging from 100 to 10,000. The RNAs of icosahedral viruses are shown to be more compact (i.e., to have smaller ?R(g)) than the random RNAs. For the random sequences we find that ?R(g) varies as N(1/3). These results are contrasted with the scaling of ?R(g) for ideal randomly branched polymers (N(1/4)), and with that from recent modeling of (relatively short, N ≤ 161) RNA tertiary structures (N(2/5)).     

Efficient calculation of α- and β-nitrogen free energies and coexistence conditions via overlap sampling with targeted perturbation

A recently introduced solid-phase free-energy calculation method that is based upon overlap sampling with targeted free-energy perturbation is further developed and extended to systems with orientational degrees of freedom. Specifically we calculate the absolute free energy of the linear-molecular nitrogen model of Etter et al., examining both the low-temperature low-pressure α-N(2) structure and the orientationally disordered β-N(2) phase. In each perturbation (for the α-N(2) phase) to determine the free-energy difference between systems at adjacent temperatures, harmonic coordinate scaling is applied to both the translational and rotational degrees of freedom in the nitrogen molecule to increase the phase-space overlap of the two perturbing systems and consequently, improve the free-energy difference results. For the plastic β-N(2) phase, a novel method that requires several perturbation paths is introduced to calculate its absolute free energy. Through these methods, the absolute free energies for both the α-N(2) and β-N(2) phase can be accurately and precisely determined. We find again that the anharmonic contribution to the free energy has weak dependence on system size. The transition properties for the α-N(2) and β-N(2) phase are also investigated. The α-β phase transition for the model at atmospheric pressure (0.1 MPa) is found to occur at 40.35 ± 0.01 K with volumetric and entropy changes of 0.44 ± 0.01 cm(3)/mol and 1.99 ± 0.01 cal/mol.K respectively.     

A highly α-stereoselective synthesis of oligosaccharide fragments of the Vi antigen from Salmonella typhi and their antigenic activities

In this paper, a convenient approach to the synthesis of the repeating α-(1→4)-linked N-acetyl galactosaminuronic acid units from the capsular polysaccharide of Salmonella typhi is reported. The exclusively α-stereoselective glycosylation reactions were achieved by using oxazolidinone-protected glycosides as building blocks based on a pre-activation protocol. Di-, tri-, and tetrasaccharides were prepared by this short and efficient approach in high yields. The enzyme-linked immunosorbent assay experiments show that our synthetic tri- and tetrasaccharide had much higher antigenic activities than previously reported ones in the inhibition of antibody binding by the native polysaccharide. The results demonstrate that the antigenic activities of saccharides can be strengthened greatly by increasing the number of acetyl groups present.     

Numerical study of the DLC film flow field in the ECR-PECVD reaction chamber

This paper mainly investigates the optimum parameters for the fabrication of uniform diamond-like carbon (DLC) films on the electron cyclotron resonance plasma enhanced chemical vapor deposition (ECR-PECVD) reaction chamber by analyzing the effect of the reacting gas velocity on the film properties. This work makes use of computational fluid dynamics (CFD) approach to model surface chemical reactions, flow and temperature fields, as well as heat and mass transfer phenomena. The simulation has shown that natural convection and mass transfer affect the recirculating flow within the reactor and, therefore, the distribution of material deposition. In other words, as a result of attaching an endplate (baffle) at the top of the substrate, the deposition rate of the substrate is appreciably enhanced. However, the surface uniformity of the substrate is obviously deteriorated.     

Vortex dynamics in the presence of excess energy for the Landau–Lifshitz–Gilbert equation

We study the Landau–Lifshitz–Gilbert equation for the dynamics of a magnetic vortex system. We present a PDE-based method for proving vortex dynamics that does not rely on strong well-preparedness of the initial data and allows for instantaneous changes in the strength of the gyrovector force due to bubbling events. The main tools are estimates of the Hodge decomposition of the supercurrent and an analysis of the defect measure of weak convergence of the stress energy tensor. Ginzburg–Landau equations with mixed dynamics in the presence of excess energy are also discussed.     

Low‐loss aluminium nitride thin film for mid‐infrared microphotonics

Mid‐infrared (mid‐IR) microphotonic devices including (i) straight/bent waveguides and (ii) Y‐junction beam splitters are developed on thin films of CMOS‐compatible sputter deposited aluminum nitride (AlN)‐on‐silicon. An optical loss of 0.83 dB/cm at λ = 2.5 µm is achieved. In addition, an efficient mid‐IR 50:50 beam splitter is demonstrated over 200 nm spectral bandwidth along with a <2% power difference between adjacent channels. With the inherent advantage of an ultra‐wide transparent window (ultraviolent to mid‐IR), our AlN mid‐IR platform can enable broadband optical networks on a chip.